title: Scanning for genomic regions subject to selective sweeps using SNP-MaP strategy.
abstract: Population genomic approaches, which take advantages of high-throughput genotyping, are powerful yet costly methods to scan for selective sweeps. DNA-pooling strategies have been widely used for association studies because it is a cost-effective alternative to large-scale individual genotyping. Here, we performed an SNP-MaP (single nucleotide polymorphism microarrays and pooling) analysis using samples from Eurasia to evaluate the efficiency of pooling strategy in genome-wide scans for selection. By conducting simulations of allelotype data, we first demonstrated that the boxplot with average heterozygosity (HET) is a promising method to detect strong selective sweeps with a moderate level of pooling error. Based on this, we used a sliding window analysis of HET to detect the large contiguous regions (LCRs) putatively under selective sweeps from Eurasia datasets. This survey identified 63 LCRs in a European population. These signals were further supported by the integrated haplotype score (iHS) test using HapMap II data. We also confirmed the European-specific signatures of positive selection from several previously identified genes(KEL, TRPV5, TRPV6, EPHB6). In summary, our results not only revealed the high credibility of SNP-MaP strategy in scanning for selective sweeps, but also provided an insight into the population differentiation.
authors.affiliation: Facuity of Basic Medical Science, Nanchang University, Nanchang 330006, China.
authors.forename: Libin
authors.initials: L
authors.lastname: Deng
authors.forename: Xiaoli
authors.initials: X
authors.lastname: Tang
authors.forename: Wei
authors.initials: W
authors.lastname: Chen
authors.forename: Jiari
authors.initials: J
authors.lastname: Lin
authors.forename: Zhiqing
authors.initials: Z
authors.lastname: Lai
authors.forename: Zuoqi
authors.initials: Z
authors.lastname: Liu
authors.forename: Dake
authors.initials: D
authors.lastname: Zhang
mesh_terms: D003198:Computer Simulation; D005828:Genetics, Population / Q000379:methods*; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D006239:Haplotypes; D006579:Heterozygote; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic; D044465:White People / Q000235:genetics